EMD-0553

Single-particle
2.4 Å
EMD-0553
3D View Gallery
Deposition: 12/02/2019
Map released: 12/06/2019
Last modified: 16/10/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-0553
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 6nz0 summary report (pdf.gz) Map and 6nz0 FULL report (pdf.gz)
EMICSS annotations (xml)

Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2

EMD-0553

Single-particle
2.4 Å
EMD-0553
3D View Gallery
Deposition: 12/02/2019
Map released: 12/06/2019
Last modified: 16/10/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.1 mg/mL
Details: Virus-like particles at 0.10 mg/mL were adhered to thin continuous carbon-coated grids, then, after initial blotting, AAVR-PKD1-2 was added at 0.74 mg/mL (a 10-fold molar excess over AAV2 subunits) before blotting again.
Buffer
pH: 7.4
Buffer components [3]:
Name Formula Concentration ChEBI
HEPES - 25.0 mM -
NaCl - 150.0 mM -
MgCl2 - 50.0 mM -
Grid
Mesh: 400
Material: COPPER
Details: Glow discharge settings: Pelco easiGlow, 25s, 25mA, 0.39mBar, negative polarity Grid: Ted Pella Cat#01824, ultrathin carbon film (<3nm) on lacey carbon support film
Pretreatment
Type: GLOW DISCHARGE
Time: 25 s
Atmosphere: AIR
Pressure: 0.039 kPa
Support Film [1]
Material Topology Thickness
CARBON LACEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 298.15 K
Instrument: FEI VITROBOT MARK IV
Details: 4ul of AAV-2 (1.7uM) was added to the grid, followed by 4ul of AAVR-PKD1-2 (16.7uM), with manual blotting after each addition with Whatman paper (Cat. no. 1001-110.) 4ul of buffer containing 25mM HEPES, 150mM NaCl, pH 7.4 was added to the grid before final blotting and plunge-freezing in the Vitrobot (blot time 1.5sec, blot force -1)..
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: -0.8 µm - -2.0 µm
Nominal magnification: 75000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: FEI FALCON III (4k x 4k)
Detector mode: SUPER-RESOLUTION
Dimensions: 7676 pixel x 7420 pixel
Number of grids: 1
Number of real images: 2329
Average exposure time: 40.0 s
Average electron dose per image: 25.4 e/Å2
Image processing [1]
Final reconstruction
Resolution: 2.4 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 21373
⌯ Applied Symmetry
Point group: I
Software [1]
Name Version Details
RELION 3.0b -
Startup model [1]
Type: OTHER
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 3.0b -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 3.0b -
Particle selection [1]
Selected Ref. model Method Software Details
34450 - - - RELION Autopicker using 3D AAV-2 reference filtered to 20A with 15 degree sampling
Final 3D classification
Number of classes: 2
Software [1]
Name Version Details
RELION 3.0b -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: EM sharpened map
⬡ Geometry
X Y Z
Origin -192 -192 -192
Dimensions (px) 384 384 384
Dimensions (Å) 401.664 401.664 401.664
Voxel size (Å) 1.046 1.046 1.046
Contour list
Primary Level Source
True 0.053 AUTHOR